A surface energy spectral study on the bone heterogeneity and beam obliquity using the flattened and unflattened photon beams

Aim

Using flattened and unflattened photon beams, this study investigated the spectral variations of surface photon energy and energy fluence in the bone heterogeneity and beam obliquity.

Background

Surface dose enhancement is a dosimetric concern when using unflattened photon beam in radiotherapy. It is because the unflattened photon beam contains more low-energy photons which are removed by the flattening filter of the flattened photon beam.

Materials and methods

We used a water and bone heterogeneity phantom to study the distributions of energy, energy fluence and mean energy of the 6 MV flattened and unflattened photon beams (field size = 10 cm × 10 cm) produced by a Varian TrueBEAM linear accelerator. These elements were calculated at the phantom surfaces using Monte Carlo simulations. The photon energy and energy fluence calculations were repeated with the beam angle turned from 0° to 15°, 30° and 45° in the water and bone phantom.

Results

Spectral results at the phantom surfaces showed that the unflattened photon beams contained more photons concentrated mainly in the low-energy range (0–2 MeV) than the flattened beams associated with a flattening filter. With a bone layer of 1 cm under the phantom surface and within the build-up region of the 6 MV photon beam, it is found that both the flattened and unflattened beams had slightly less photons in the energy range <0.4 MeV compared to the water phantom. This shows that the presence of the bone decreased the low-energy photon backscatters to the phantom surface. When both the flattened and unflattened photon beams were rotated from 0° to 45°, the number of photon and mean photon energy increased. This indicates that both photon beams became more hardened or penetrate when the beam angle increased. In the presence of bone, the mean energies of both photon beams increased. This is due to the absorption of low-energy photons by the bone, resulting in more beam hardening.

Conclusions

This study explores the spectral relationships of surface photon energy and energy fluence with bone heterogeneity and beam obliquity for the flattened and unflattened photon beams. The photon spectral information is important in studies on the patient''s surface dose enhancement using unflattened photon beams in radiotherapy.     

A depth dose study between AAA and AXB algorithm against Monte Carlo simulation using AIP CT of a 4D dataset from a moving phantom

Aim

To identifying depth dose differences between the two versions of the algorithms using AIP CT of a 4D dataset.

The determination of a dose deposited in reference medium due to (p,n) reaction occurring during proton therapy

AimThe aim of the investigation was to determine the undesirable dose coming from neutrons produced in reactions (p,n) in irradiated tissues represented by water.BackgroundProduction of neutrons in the system of beam collimators and in irradiated tissues is the undesirable phenomenon related to the application of protons in radiotherapy. It makes that proton beams are contaminated by neutrons and patients receive the undesirable neutron dose.Materials and methodsThe investigation was based on the Monte Carlo simulations (GEANT4 code). The calculations were performed for five energies of protons: 50 MeV, 55 MeV, 60 MeV, 65 MeV and 75 MeV. The neutron doses were calculated on the basis of the neutron fluence and neutron energy spectra derived from simulations and by means of the neutron fluence–dose conversion coefficients taken from the ICRP dosimetry protocol no. 74 for the antero-posterior irradiation geometry.ResultsThe obtained neutron doses are much less than the proton ones. They do not exceed 0.1%, 0.4%, 0.5%, 0.6% and 0.7% of the total dose at a given depth for the primary protons with energy of 50 MeV, 55 MeV, 60 MeV, 65 MeV and 70 MeV, respectively.ConclusionsThe neutron production takes place mainly along the central axis of the beam. The maximum neutron dose appears at about a half of the depth of the maximum proton dose (Bragg peak), i.e. in the volume of a healthy tissue. The doses of neutrons produced in the irradiated medium (water) are about two orders of magnitude less than the proton doses for the considered range of energy of protons.     

Effect of anode angle on photon beam spectra and depth dose characteristics for X-RAD320 orthovoltage unit

Background

In radiation therapy with orthovoltage units, the tube design has a crucial effect on its dosimetric features.

Aim

In this study, the effect of anode angle on photon beam spectra, depth dose and photon fluence per initial electron was studied for a commercial orthovoltage unit of X-RAD320 biological irradiator.

Materials and methods

The MCNPX MC code was used for modeling in the current study. We used the Monte Carlo method to model the X-RAD320 X-ray unit based on the manufacturer provided information. The MC model was validated by comparing the MC calculated photon beam spectra with the results of SpekCalc software. The photon beam spectra were calculated for anode angles from 15 to 35 degrees. We also calculated the percentage depth doses for some angles to verify the impact of anode angle on depth dose. Additionally, the heel effect and its relation with anode angle were studied for X-RAD320 irradiator.

Results

Our results showed that the photon beam spectra and their mean energy are changed significantly with anode angle and the optimum anode angle of 30 degrees was selected based on less heel effect and appropriate depth dose and photon fluence per initial electron.

Conclusion

It can be concluded that the anode angle of 30 degrees for X-RAD320 unit used by manufacturer has been selected properly considering the heel effect and dosimetric properties.     

Effect of air cavities on the dose delivered to the lung during high-dose brachytherapy

In the treatment of lung cancer using the radiotherapy technique of intracavitary brachytherapy with an¹⁹²Ir source, the lung is normally assumed to be entirely composed of a homogenous mass of soft tissue. The aim of this study is to investigate whether there is the possibility that the air cavities in the lung influence the dose delivered to the lung at a prescribed distance from the source. The Monte Carlo code MCNP-4A was used to model the dose delivered by both¹⁹²Ir and¹⁹⁸Au as a function of treatment medium, density and composition, photon energy, and distance from the source. The suitability of MCNP-4A for this study was tested by producing depth-dose profiles for photons in water and comparing these to calculated profiles produced using well-documented methods.     

Monte Carlo Simulations of the Chemical Potential and Free Energy for Trimer and Hexamer Rings

Abstract

The chemical potential of a trimer and hexamer model ring system was determined by computer simulation over a range of temperatures and densities. Such ring molecules are important as model aromatic and naphthenic hydrocarbons. Thermodynamic integration of the pressure along a reversible path, Widom's ghost particle insertion method and Kirkwood's charging parameter method were used over a molecular density range of 0.05 to 0.30. Data were obtained by Monte Carlo simulation of a 96 molecule system that was modelled with a Lennard-Jones 6-12 truncated potential. The original insertion method, which does not take into account the orientation of the molecule when it is inserted, gives results for the chemical potential which deviate from that obtained using the thermodynamic pressure integration. At high density or temperature the deviation is significant. We have modified the Widom insertion technique to account for this short range orientation and find good agreement between this technique and the thermodynamic integration method for the chemical potential. We also calculated the free energy difference between our model ring molecules and ring molecules made up of hard spheres.     

Generating and using patient-specific whole-body models for organ dose estimates in CT with increased accuracy: Feasibility and validation

The estimation of patient dose using Monte Carlo (MC) simulations based on the available patient CT images is limited to the length of the scan. Software tools for dose estimation based on standard computational phantoms overcome this problem; however, they are limited with respect to taking individual patient anatomy into account. The purpose of this study was to generate whole-body patient models in order to take scattered radiation and over-scanning effects into account. Thorax examinations were performed on three physical anthropomorphic phantoms at tube voltages of 80 kV and 120 kV; absorbed dose was measured using thermoluminescence dosimeters (TLD). Whole-body voxel models were built as a combination of the acquired CT images appended by data taken from widely used anthropomorphic voxel phantoms. MC simulations were performed both for the CT image volumes alone and for the whole-body models. Measured and calculated dose distributions were compared for each TLD chip position; additionally, organ doses were determined.MC simulations based only on CT data underestimated dose by 8%–15% on average depending on patient size with highest underestimation values of 37% for the adult phantom at the caudal border of the image volume. The use of whole-body models substantially reduced these errors; measured and simulated results consistently agreed to better than 10%.This study demonstrates that combined whole-body models can provide three-dimensional dose distributions with improved accuracy. Using the presented concept should be of high interest for research studies which demand high accuracy, e.g. for dose optimization efforts.     

A Modified Valley Restrained Monte Carlo Method to Efficiently Search the Low Energy Structures of Peptides

Abstract

A new Monte Carlo sampling scheme, namely the Modified Valley Restrained Monte Carlo procedure, is used to obtain the global energy minimum conformations for polypeptides, such as Met-enkephalin and Melittin. For each peptide, we found close agreement with previous results from both theoretical and experimental studies. The simple idea for controlling the step size according to the Valley Function, provides useful suggestions in searching the global energy minimum structures, and furthermore helps solve the multiple minima problem.     

Monte Carlo evaluation of the dose calculation algorithm of TomoTherapy for clinical cases in dynamic jaws mode

PurposeFor the TomoTherapy^® system, longitudinal conformation can be improved by selecting a smaller field width but at the expense of longer treatment time. Recently, the TomoEdge^® feature has been released with the possibility to move dynamically the jaws at the edges of the target volume, improving longitudinal penumbra and enabling faster treatments. Such delivery scheme requires additional modeling of treatment delivery. Using a previously validated Monte Carlo model (TomoPen), we evaluated the accuracy of the implementation of TomoEdge in the new dose engine of TomoTherapy for 15 clinical cases.MethodsTomoPen is based on PENELOPE. Particle tracking in the treatment head is performed almost instantaneously by 1) reading a particle from a phase-space file corresponding to the largest field and 2) correcting the weight of the particle depending on the actual jaw and MLC configurations using Monte Carlo pre-generated data. 15 clinical plans (5 head-and-neck, 5 lung and 5 prostate tumors) planned with TomoEdge and with the last release of the treatment planning system (VoLO^®) were re-computed with TomoPen. The resulting dose-volume histograms were compared.ResultsGood agreement was achieved overall, with deviations for the target volumes typically within 2% (D₉₅), excepted for small lung tumors (17 cm³) where a maximum deviation of 4.4% was observed for D₉₅. The results were consistent with previously reported values for static field widths.ConclusionsFor the clinical cases considered in the present study, the introduction of TomoEdge did not impact significantly the accuracy of the computed dose distributions.     

Estimation of Free Energy Systematic Errors in Molecular Simulations of Globular Proteins Surrounded by Finite Water Clusters. One Center Multipole Expansion of Reaction Field Differences

Free energy calculated in simulations on the atomic level (Monte Carlo or Molecular Dynamics) has a systematic error, if the water shell surrounding a globular protein is finite. The error (“cluster error”) is equal to a difference of free energies obtained in simulations with an infinite and finite water shell. In this work a continuum dielectric model was used to estimate the “cluster error”. A multipole expansion of the estimate was performed for a water shell with a spherical outer boundary. The expansion has very simple form. Each term is a product of two functions, one of them depending only on the charge's conformation, and the other one only on dielectric properties of the system. There are two practical uses of the expansion. First, it may be used to estimate the “cluster error” in a simulation already made; second, it may be used to plan a simulation in such a way that the “cluster error” is minimal. Numerical values of the largest terms in the multipole expansion corresponding to a typical system in simulations of globular proteins are given.     

Dosimetric impact of statistical uncertainty on Monte Carlo dose calculation algorithm in volumetric modulated arc therapy using Monaco TPS for three different clinical cases

AimTo study the dosimetric impact of statistical uncertainty (SU) per plan on Monte Carlo (MC) calculation in Monaco? treatment planning system (TPS) during volumetric modulated arc therapy (VMAT) for three different clinical cases.BackgroundDuring MC calculation SU is an important factor to decide dose calculation accuracy and calculation time. It is necessary to evaluate optimal acceptance of SU for quality plan with reduced calculation time.Materials and methodsThree different clinical cases as the lung, larynx, and prostate treated using VMAT technique were chosen. Plans were generated with Monaco? V5.11 TPS with 2% statistical uncertainty. By keeping all other parameters constant, plans were recalculated by varying SU, 0.5%, 1%, 2%, 3%, 4%, and 5%. For plan evaluation, conformity index (CI), homogeneity index (HI), dose coverage to PTV, organ at risk (OAR) dose, normal tissue receiving dose ≥5 Gy and ≥10 Gy, integral dose (NTID), calculation time, gamma pass rate, calculation reproducibility and energy dependency were analyzed.ResultsCI and HI improve as SU increases from 0.5% to 5%. No significant dose difference was observed in dose coverage to PTV, OAR doses, normal tissue receiving dose ≥5 Gy and ≥10 Gy and NTID. Increase of SU showed decrease in calculation time, gamma pass rate and increase in PTV max dose. No dose difference was seen in calculation reproducibility and dependent on energy.ConclusionFor VMAT plans, SU can be accepted from 1% to 3% per plan with reduced calculation time without compromising plan quality and deliverability by accepting variations in point dose within the target.     

Atomistic simulations of the effects of polyglutamine chain length and solvent quality on conformational equilibria and spontaneous homodimerization

Aggregation of expanded polyglutamine tracts is associated with nine different neurodegenerative diseases, including Huntington's disease. Experiments and computer simulations have demonstrated that monomeric forms of polyglutamine molecules sample heterogeneous sets of collapsed structures in water. The current work focuses on a mechanistic characterization of polyglutamine homodimerization as a function of chain length and temperature. These studies were carried out using molecular simulations based on a recently developed continuum solvation model that was designed for studying conformational and binding equilibria of intrinsically disordered molecules such as polyglutamine systems. The main results are as follows: Polyglutamine molecules form disordered, collapsed globules in aqueous solution. These molecules spontaneously associate at conditions approaching those of typical in vitro experiments for chains of length N ≥ 15. The spontaneity of these homotypic associations increases with increasing chain length and decreases with increasing temperature. Similar and generic driving forces govern both collapse and spontaneous homodimerization of polyglutamine in aqueous milieus. Collapse and dimerization maximize self-interactions and reduce the interface between polyglutamine molecules and the surrounding solvent. Other than these generic considerations, there do not appear to be any specific structural requirements for either chain collapse or chain dimerization; that is, both collapse and dimerization are nonspecific in that disordered globules form disordered dimers. In fact, it is shown that the driving force for intermolecular associations is governed by spontaneous conformational fluctuations within monomeric polyglutamine. These results suggest that polyglutamine aggregation is unlikely to follow a homogeneous nucleation mechanism with the monomer as the critical nucleus. Instead, the results support the formation of disordered, non-β-sheet-like soluble molten oligomers as early intermediates—a proposal that is congruent with recent experimental data.     

Energy migration as related to the mutual position and orientation of donor and acceptor molecules in LH1 and LH2 antenna complexes of purple bacteria

Many approaches to discovering the interaction energy of molecular transition dipoles use the well-known coefficient xi(phi, psi (1) psi (2)) = (cos phi - 3 cos psi (1) cos psi (2))(2), where phi, Psi (1), and Psi (2) are inter-dipole angles. Unfortunately, this formula often yields rather approximate results, in particular, when it is applied to closely positioned molecules. This problem is of great importance when dealing with energy migration in photosynthetic organisms, because the major part of excitation transfers in their chlorophyllous antenna proceed between closely positioned molecules. In this paper, the authors introduce corrected values of the orientation factor for several types of mutual orientation of molecules exchanging with electronic excitations for realistic ratios of dipole lengths and spacing. The corrected magnitudes of interaction energies of neighboring bacteriochlorophyll molecules in LH2 and LH1 light-absorbing complexes are calculated for the class of photosynthetic purple bacteria. Some advantageous factors are revealed in their mutual positions and orientations in vivo.     

Development of Dual Ensemble Monte Carlo Program and its Application to the CO2/N2 Separation

Abstract

A novel Monte Carlo simulation named as Dual Ensemble Monte Carlo (DEMC) method is developed for the investigation of the membrane separation process. In this method the spatial combination of Grand Canonical MC and Canonical MC techniques is employed. The DEMC method can be used to calculate the separation factor at a specific chemical potential gradient. At first, a check on the accuracy of the DEMC method is made by generating gas density gradient between two reservoir regions. Thereafter, we applied this method to CO₂/N₂ gas separation by inorganic membranes and calculated the separation factor dependence on the size of micropore in membranes.     

Measurement and comparison of head scatter factor for 7 MV unflattened (FFF) and 6 MV flattened photon beam using indigenously designed columnar mini phantom

Aim

To measure and compare the head scatter factor for 7 MV unflattened and 6 MV flattened photon beam using a home-made designed mini phantom.

Background

The head scatter factor (Sc) is one of the important parameters for MU calculation. There are multiple factors that influence the Sc values, like accelerator head, flattening filter, primary and secondary collimators.

Materials and methods

A columnar mini phantom was designed as recommended by AAPM Task Group 74 with high and low atomic number material for measurement of head scatter factors at 10 cm and d_max dose water equivalent thickness.

Results

The Sc values measured with high-Z are higher than the low-Z mini phantoms observed for both 6MV-FB and 7MV-UFB photon energies. Sc values of 7MV-UFB photon beams were smaller than those of the 6MV-FB photon beams (0.6–2.2% (Primus), 0.2–1.4% (Artiste) and 0.6–3.7% (Clinac iX (2300CD))) for field sizes ranging from 10 cm × 10 cm to 40 cm × 40 cm. The SSD had no influence on head scatter for both flattened and unflattened beams. The presence of wedge filters influences the Sc values. The collimator exchange effects showed that the opening of the upper jaw increases Sc irrespective of FF and FFF.

Conclusions

There were significant differences in Sc values measured for 6MV-FB and unflattened 7MV-UFB photon beams over the range of field sizes from 10 cm × 10 cm to 40 cm × 04 cm. Different results were obtained for measurements performed with low-Z and high-Z mini phantoms.     

Proton relaxation enhancement in tissue due to ingested manganese chloride: time course and dose response in the rat

MnCl2, a potential NMR contrast agent, was force fed by cannula to 27 fasted rats in an attempt to establish the efficacy of this route of administration. The animals were sacrificed and the relaxation times (T1 and T2) of liver, spleen, kidney, heart, and skeletal muscle were determined in vitro. One group of rats was subject to a range of doses (8.3-333.3 mg/kg) and sacrificed at 90 minutes. Another group received a single large dose (500 mg/kg) with animals sacrificed at intervals from 15-225 minutes. The single large dose caused a rapid and prolonged reduction in liver T1 (-93% of normal) and to a lesser degree affected the other organs. The dose response data shows that liver T1 is also affected at significantly lower dosages than the other tissues tested. These results suggest the oral route as a possible alternative to IV Mn+2. Further studies with inorganic and organic manganese are indicated.     

The influence of the medical care on the human life expectancy in 20th century and the Penna ageing model

Summary The expression of many genetic defects may be suppressed by proper medical care or even by changing the environmental conditions. We have used the Penna model of ageing to show that such efFects may be responsible for increasing the human life expectancy during the 20 ^th century. This effect is equivalent to the shift of the threshold (T) in the Penna model, which determines how many deleterious, expressed mutations kill an organism. For long genomes, the shift of T changes the age distribution significantly with negligible relative changes in the maximum life span, while for short genomes, the shift of T changes both, the age distribution as well as the maximum age. Unfortunately the same simulations show that the strategy of enhancing the medical care requires more and more effort to keep the mortality rate of our populations at the same lower level and that some new defects could be exposed to selection.     

Perturbation experiments and fluctuation enhancement in finite size of lattice ecosystems: Uncertainty in top-predator conservation

Study of perturbation experiments is crucial for conservation biology. We carry out Monte Carlo simulations on finite-size lattices composed of n species (n ≤ 4). The value of mortality rate m of top predator is altered to a higher or lower level, and a fluctuation enhancement (FE) is explored. Here FE means an uncertainty in population dynamics. It is found for n ≥ 2 that FE is observed, when m is decreased. Namely, when we protect the top predator, its population dynamics becomes very difficult to predict.     

Empirical solvation models in the context of conformational energy searches: application to bovine pancreatic trypsin inhibitor.

Continuum solvation models that estimate free energies of solvation as a function of solvent accessible surface area are computationally simple enough to be useful for predicting protein conformation. The behavior of three such solvation models has been examined by applying them to the minimization of the conformational energy of bovine pancreatic trypsin inhibitor. The models differ only with regard to how the constants of proportionality between free energy and surface area were derived. Each model was derived by fitting to experimentally measured equilibrium solution properties. For two models, the solution property was free energy of hydration. For the third, the property was NMR coupling constants. The purpose of this study is to determine the effect of applying these solvation models to the nonequilibrium conformations of a protein arising in the course of global searches for conformational energy minima. Two approaches were used: (1) local energy minimization of an ensemble of conformations similar to the equilibrium conformation and (2) global search trajectories using Monte Carlo plus minimization starting from a single conformation similar to the equilibrium conformation. For the two models derived from free energy measurements, it was found that both the global searches and local minimizations yielded conformations more similar to the X-ray crystallographic structures than did searches or local minimizations carried out in the absence of a solvation component of the conformational energy. The model derived from NMR coupling constants behaved similarly to the other models in the context of a global search trajectory. For one of the models derived from measured free energies of hydration, it was found that minimization of an ensemble of near-equilibrium conformations yielded a new ensemble in which the conformation most similar to the X-ray determined structure PTI4 had the lowest total free energy. Despite the simplicity of the continuum solvation models, the final conformation generated in the trajectories for each of the models exhibited some of the characteristics that have been reported for conformations obtained from molecular dynamics simulations in the presence of a bath of explicit water molecules. They have smaller root mean square (rms) deviations from the experimentally determined conformation, fewer incorrect hydrogen bonds, and slightly larger radii of gyration than do conformations derived from search trajectories carried out in the absence of solvent.